No, I'm not making another guess about who Cartman's dad is. I'm just raising the question of whether they may have filmed more than one ending for this episode. Say maybe they had originally planned it to be the alien. Well, now that everyone on the newgroup knows about the hidden alien, it wouldn't be as shocking (read: funny) if this actually turned out to be true. Maybe Parker & Stone or someone on the SP staff has been checking out all of our speculation just to make sure we don't stumble upon the answer and spoil their surprise.
This is precisely what The Simpsons did with "Who Shot Mr. Burns" (although they hid the real ending from most of their staff as well) so if it's true, maybe one day we'll get to see outtakes of the alternate endings.